updated readthedocs

docs/api.rst

@@ -4,6 +4,36 @@ API Reference
 This page documents the main classes and functions for computing electric fields,
 electrostatic potentials, and partial charges.
 
+.. _quick-reference:
+
+Quick Reference
+---------------
+
+.. list-table::
+   :widths: 20 35 25 20
+   :header-rows: 1
+
+   * - Function
+     - Key Inputs
+     - Output
+     - Requirements
+   * - :ref:`getEfield() <getefield-electric-field>`
+     - ``charge_types``, ``input_bond_indices``, ``multiwfn_path``
+     - DataFrame with E-field (V/Å)
+     - Molden + XYZ files
+   * - :ref:`getESP() <getesp-electrostatic-potential>`
+     - ``charge_types``, ``multiwfn_path``
+     - DataFrame with ESP (V)
+     - ``esp_atom_idx`` at init
+   * - :ref:`getCharges() <getcharges-partial-charges>`
+     - ``charge_types``, ``multiwfn_path``, ``write_pdb``
+     - DataFrame with charges
+     - Molden + XYZ files
+   * - :ref:`getElectrostatic_stabilization() <getelectrostatic-stabilization-electrostatic-stabilization>`
+     - ``substrate_idxs``, ``charge_type``, ``multipole_order``
+     - DataFrame with energies (kcal/mol)
+     - Molden + XYZ files
+
 Electrostatics Class
 --------------------
 
@@ -19,8 +49,7 @@ Initialization
    es = Electrostatics(
        molden_paths,      # List of .molden file paths
        xyz_paths,         # List of .xyz file paths
-       lst_of_tmcm_idx=None,  # Metal atom indices for ESP (0-indexed)
-       dielectric=1,      # Dielectric constant
+       esp_atom_idx=None, # Atom indices for ESP (0-indexed)
        ptchg_paths=None   # Point charge files for QM/MM
    )
 
@@ -31,10 +60,11 @@ Initialization
 
 **Optional parameters:**
 
-- ``lst_of_tmcm_idx`` (list of int): Metal atom indices for ESP calculations
-- ``dielectric`` (float): Dielectric constant (1=vacuum, 4=protein, 78.5=water)
+- ``esp_atom_idx`` (list of int): Atom indices for ESP calculations (0-indexed)
 - ``ptchg_paths`` (list): Point charge file paths for QM/MM calculations
 
+.. _getefield-electric-field:
+
 getEfield() - Electric Field
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -60,6 +90,8 @@ getEfield() - Electric Field
 
 **Returns:** DataFrame with electric field results
 
+.. _getesp-electrostatic-potential:
+
 getESP() - Electrostatic Potential
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -83,16 +115,92 @@ getESP() - Electrostatic Potential
 
 **Returns:** DataFrame with ESP results
 
-**Note:** Requires ``lst_of_tmcm_idx`` to be set during initialization.
+**Note:** Requires ``esp_atom_idx`` to be set during initialization.
+
+.. _getcharges-partial-charges:
+
+getCharges() - Partial Charges
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: python
+
+   df = es.getCharges(
+       charge_types='Hirshfeld_I',  # Charge scheme(s)
+       multiwfn_path='/path/to/multiwfn',
+       output_filename='charges',   # Output filename prefix
+       write_pdb=False              # Write PDB files with charges
+   )
+
+**Parameters:**
+
+- ``charge_types`` (str or list): Charge scheme(s) to use
+- ``multiwfn_path`` (str): Path to Multiwfn executable
+- ``output_filename`` (str): Output CSV filename prefix
+- ``write_pdb`` (bool): If True, write PDB files with charges in B-factor column
+
+**Returns:** DataFrame with columns: Job, Charge_Type, Atom_Index, Element, x, y, z, Charge, Molden_Path, XYZ_Path
+
+.. _getelectrostatic-stabilization-electrostatic-stabilization:
+
+getElectrostatic_stabilization() - Electrostatic Stabilization
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: python
+
+   df = es.getElectrostatic_stabilization(
+       multiwfn_path='/path/to/multiwfn',
+       substrate_idxs=[],           # Substrate atom indices per structure
+       charge_type='Hirshfeld_I',   # Charge scheme
+       multipole_order=2,           # 1 for monopole, 2 for dipole
+       dielectric=1                 # Dielectric constant
+   )
+
+**Parameters:**
+
+- ``multiwfn_path`` (str): Path to Multiwfn executable
+- ``substrate_idxs`` (list): List of atom indices for substrate per structure
+- ``charge_type`` (str): Charge scheme (Hirshfeld, Hirshfeld_I, or Becke for multipole_order=2)
+- ``multipole_order`` (int): 1 for monopole, 2 for dipole corrections
+- ``dielectric`` (float): Dielectric constant
+
+**Returns:** DataFrame with electrostatic stabilization energies
 
 Charge Schemes
 --------------
 
 **Available schemes:**
 
-- Hirshfeld, Hirshfeld_I, Voronoi, Mulliken, Lowdin
-- SCPA, Becke, ADCH, CHELPG, MK, AIM
-- CM5, EEM, RESP, PEOE
++---------------+------------------------------------------+--------------------------------------------------+
+| Charge Type   | Description                              | Notes                                            |
++===============+==========================================+==================================================+
+| Hirshfeld_I   | Iterative Hirshfeld                      | Recommended for most systems                     |
++---------------+------------------------------------------+--------------------------------------------------+
+| Hirshfeld     | Standard Hirshfeld partitioning          | Fast, good for most systems                      |
++---------------+------------------------------------------+--------------------------------------------------+
+| RESP          | Restrained ESP fitting                   | Standard for force field development             |
++---------------+------------------------------------------+--------------------------------------------------+
+| CHELPG        | ESP fitting (Breneman)                   | Good for molecular mechanics                     |
++---------------+------------------------------------------+--------------------------------------------------+
+| MK            | Merz-Kollmann ESP fitting                | Alternative ESP method                           |
++---------------+------------------------------------------+--------------------------------------------------+
+| CM5           | Charge Model 5                           | Good balance of accuracy/speed                   |
++---------------+------------------------------------------+--------------------------------------------------+
+| ADCH          | Atomic dipole corrected Hirshfeld        | Recommended by Multiwfn                          |
++---------------+------------------------------------------+--------------------------------------------------+
+| Mulliken      | Mulliken population                      | Fast but basis-set dependent                     |
++---------------+------------------------------------------+--------------------------------------------------+
+| Lowdin        | Löwdin population                        | Orthogonalized basis                             |
++---------------+------------------------------------------+--------------------------------------------------+
+| Voronoi       | Voronoi deformation density              | Space partitioning method                        |
++---------------+------------------------------------------+--------------------------------------------------+
+| SCPA          | Ros & Schuit modified Mulliken           | Modified Mulliken scheme                         |
++---------------+------------------------------------------+--------------------------------------------------+
+| Becke         | Becke partitioning with dipole corr.     | Real-space integration                           |
++---------------+------------------------------------------+--------------------------------------------------+
+| EEM           | Electronegativity equalization           | ⚠️ Requires bonded atoms (fails for ionic)       |
++---------------+------------------------------------------+--------------------------------------------------+
+| PEOE          | Gasteiger charges                        | ⚠️ Missing parameters for Na, transition metals  |
++---------------+------------------------------------------+--------------------------------------------------+
 
 **Multipole-capable schemes** (for ``multipole_bool=True`` or ``use_multipole=True``):
 

docs/conf.py

@@ -23,7 +23,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "PyEF"
-copyright = '{}, <a href="https://kastner.io/en/">Melissa Manetsch and David W. Kastner</a>'.format(
+copyright = '{}, Melissa Manetsch and David W. Kastner'.format(
     datetime.datetime.now().year
 )
 author = "Melissa Manetsch and David W. Kastner"
@@ -98,7 +98,7 @@
 html_theme = "revitron_sphinx_theme"
 html_theme_options = {
     "navigation_depth": 5,
-    "github_url": "https://github.com/davidkastner/pyef",
+    "github_url": "https://github.com/hjkgrp/pyEF",
     "color_scheme": "dark",
 }